Snakemake reports non-zero error code when checkpoints execute successfully

[Ben Siranosian]

This affects checkpoint medaka_ranges, checkpoint pilon_ranges, checkpoint extract_bigtigs

Snakemake will exit even though the command executed successfully. For now, the only way I see around this is to execute the command in the shell manually.

This is a known issue, see: https://bitbucket.org/snakemake/snakemake/issues/1303/snakemake-checkpoint-throws-exited-with